multiple whole genome alignment tool

Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for
pairwise alignment, a custom graph based segmentation procedure for
identifying collinear regions, and the segment-based progressive
multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft
genomes in the form of multi-FASTA files and does not require a
reference genome.

The input to Mugsy is DNA from two or more genomes in FASTA
format. The genomes must be assembled into contigs or scaffolds. For
draft genomes, a single multi-FASTA file containing all contigs for
the genome should be provided.

This example will align three genomes and output a file
/data/output/mygenomes.maf. The --directory setting is also used for
storing temporary files during the run.

The prefix of each input filename will be used as the genome name in
the output files (eg. genome1 from genome1.fsa). Header lines in the
FASTA files should not contain ':' or '-' to avoid parsing problems.

View or parse MAF output

The output of Mugsy is Multiple Alignment Format
(MAF).
One option for browsing is GMAJ, which provides a
reference-based stand-alone viewer for MAF files.